Package uk.ac.cam.ch.wwmm.opsin

Class NameToStructure

  • public class NameToStructure
extends java.lang.Object
    The "master" class, to turn a name into a structure.
    Author:
    ptc24, dl387

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static NameToStructure getInstance()  
      static ParseRules getOpsinParser()
      Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name.
      static java.lang.String getVersion()
      Returns the version of the OPSIN library
      OpsinResult parseChemicalName​(java.lang.String name)
      Parses a chemical name, returning an OpsinResult which represents the molecule.
      OpsinResult parseChemicalName​(java.lang.String name, NameToStructureConfig n2sConfig)
      Parses a chemical name, returning an OpsinResult which represents the molecule.
      java.lang.String parseToCML​(java.lang.String name)
      Convenience method for converting a name to CML with OPSIN's default options
      java.lang.String parseToSmiles​(java.lang.String name)
      Convenience method for converting a name to SMILES with OPSIN's default options

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Method Detail

      • getVersion

        public static java.lang.String getVersion()
        Returns the version of the OPSIN library
        Returns:
        Version number String

      • parseToCML

        public java.lang.String parseToCML​(java.lang.String name)
        Convenience method for converting a name to CML with OPSIN's default options
        Parameters:
        name - The chemical name to parse.
        Returns:
        A CML element, containing the parsed molecule, or null if the name was uninterpretable.

      • parseToSmiles

        public java.lang.String parseToSmiles​(java.lang.String name)
        Convenience method for converting a name to SMILES with OPSIN's default options
        Parameters:
        name - The chemical name to parse.
        Returns:
        A SMILES string describing the parsed molecule, or null if the name was uninterpretable.

      • parseChemicalName

        public OpsinResult parseChemicalName​(java.lang.String name)
        Parses a chemical name, returning an OpsinResult which represents the molecule. This object contains in the status whether the name was parsed successfully A message which may contain additional information if the status was warning/failure The OpsinResult has methods to generate a SMILES or CML representation For InChI, the OpsinResult should be given to the NameToInchi class
        Parameters:
        name - The chemical name to parse.
        Returns:
        OpsinResult

      • parseChemicalName

        public OpsinResult parseChemicalName​(java.lang.String name,
                                     NameToStructureConfig n2sConfig)
        Parses a chemical name, returning an OpsinResult which represents the molecule. This object contains in the status whether the name was parsed successfully A message which may contain additional information if the status was warning/failure CML and SMILES representations may be retrieved directly from the object InChI may be generate using NameToInchi
        Parameters:
        name - The chemical name to parse.
        n2sConfig - Options to control how OPSIN interprets the name.
        Returns:
        OpsinResult

      • getOpsinParser

        public static ParseRules getOpsinParser()
        Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name. Just because a word can be split into tokens does not mean the word constitutes a valid chemical name e.g. ester is interpretable but is not in itself a chemical name
        Returns:
        Opsin parser for recognition/parsing of a chemical word